def load_effects(manifest_path, database, **kwargs):
manifest = ManifestReader(manifest_path)
vcf_info = manifest.section('vcf')
# No data regarding VCF
if 'file' not in vcf_info:
return
cursor = connections[database].cursor()
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
with open(vcf_path) as fin:
log.debug("opening {0} in {1} load_effects".format(vcf_path, __name__))
stream = EffectStream(fin)
columns = stream.output_columns
db_table = VariantEffect._meta.db_table
pgcopy_batch(stream, db_table, columns, cursor, database)
def load_effects(manifest_path, database, **kwargs):
manifest = ManifestReader(manifest_path)
vcf_info = manifest.section('vcf')
# No data regarding VCF
if 'file' not in vcf_info:
return
cursor = connections[database].cursor()
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
with open(vcf_path) as fin:
log.debug("opening {0} in {1} load_effects".format(vcf_path, __name__))
stream = EffectStream(fin)
columns = stream.output_columns
db_table = VariantEffect._meta.db_table
pgcopy_batch(stream, db_table, columns, cursor, database)
def load_variants(manifest_path, database, **kwargs):
"Variant loading requires only a VCF file and will never load a duplicate."
manifest = ManifestReader(manifest_path)
vcf_info = manifest.section('vcf')
# No data regarding VCF
if 'file' not in vcf_info:
return
cursor = connections[database].cursor()
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
with open(vcf_path) as fin:
log.debug("opening {0} in {1}".format(vcf_path, __name__))
stream = VariantStream(fin)
columns = stream.output_columns
db_table = Variant._meta.db_table
pgcopy_batch(stream, db_table, columns, cursor, database)
VARIANT_CHANNEL.publish(manifest_path=manifest_path, database=database)
def load_variants(manifest_path, database, **kwargs):
"Variant loading requires only a VCF file and will never load a duplicate."
manifest = ManifestReader(manifest_path)
vcf_info = manifest.section('vcf')
# No data regarding VCF
if 'file' not in vcf_info:
return
cursor = connections[database].cursor()
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
with open(vcf_path) as fin:
log.debug("opening {0} in {1}".format(vcf_path, __name__))
stream = VariantStream(fin)
columns = stream.output_columns
db_table = Variant._meta.db_table
pgcopy_batch(stream, db_table, columns, cursor, database)
VARIANT_CHANNEL.publish(manifest_path=manifest_path, database=database)
def load_samples(manifest_path, database, **kwargs):
manifest = ManifestReader(manifest_path)
# Ensure the sample is marked to be loaded..
if not manifest.marked_for_load():
log.info('Sample not marked for load', extra={
'manifest_path': manifest_path,
})
return
# Ensure the sample section is valid..
if not check_sample_section(manifest):
log.info('Manifest sample section is not valid', extra={
'manifest_path': manifest_path,
})
return
# [sample]
# project = PCGC
# batch = OTHER
# sample = 1-03131
# version = 1
sample_info = manifest.section('sample')
vcf_info = manifest.section('vcf')
# ignore whatever sample is listed in the manifest and scan the vcf
# for samples
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
with open(vcf_path) as file_obj:
log.debug("opening {0} in load_samples".format(vcf_path))
reader = vcf.Reader(file_obj)
samples = reader.samples
if 'sample' in sample_info:
pretty_names = sample_info['sample'].split(',')
else:
pretty_names = samples
if len(samples) != len(pretty_names):
log.info('Length of comma-delimited samples field in manifest '
'does not match the length of samples in {0}'
.format(vcf_info['file']))
return
# Create the sample (and batch and project if needed)..
num_created = 0
num_skipped = 0
for pretty_name, vcf_sample in zip(pretty_names, samples):
log.debug('Trying to create {0} sample record'.format(vcf_sample))
sample, created = create_sample(sample_name=pretty_name,
vcf_colname=vcf_sample,
batch_name=sample_info['batch'],
project_name=sample_info['project'],
version=sample_info['version'])
log.debug('{0} created'.format(sample))
if created:
num_created += 1
sts.transition(sample, 'Sample Record Created')
else:
num_skipped += 1
manifest = SampleManifest.objects.filter(sample=sample)
# Create a manfiest object for the sample if one does not exist
if created or not manifest.exists():
sample_manifest = SampleManifest(sample=sample)
sample_manifest.load_content(manifest_path)
sample_manifest.save()
sts.transition(sample, 'Sample Manifest Created')
# Publish to channel that this manifest is eligible for processing
# downstream..
if num_created > 0 or kwargs.get('force', False):
SAMPLE_CHANNEL.publish(manifest_path=manifest_path, database=database)
# Returns whether the sample has been created
load_dict = {'created': num_created, 'skipped': num_skipped}
return load_dict
def load_results(manifest_path, database, **kwargs):
manifest = ManifestReader(manifest_path)
if not manifest.marked_for_load():
log.info('Sample not marked for load', extra={
'manifest_path': manifest_path,
})
return
# Ensure the sample section is valid..
if not check_sample_section(manifest):
log.info('Manifest sample section is not valid', extra={
'manifest_path': manifest_path,
})
return
sample_info = manifest.section('sample')
vcf_info = manifest.section('vcf')
# Ignore whatever sample is listed in the manifest and scan the vcf for
# samples.
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
with open(vcf_path) as file_obj:
log.debug("opening {0} in load_samples".format(vcf_path))
reader = vcf.Reader(file_obj)
samples = reader.samples
if 'sample' in sample_info:
pretty_names = sample_info['sample'].split(',')
else:
pretty_names = samples
for pretty_name, vcf_sample in zip(pretty_names, samples):
try:
sample = Sample.objects.get(
name__iexact=pretty_name,
batch__name__iexact=sample_info['batch'],
project__name__iexact=sample_info['project'],
version=sample_info['version'])
except Sample.DoesNotExist:
log.error('Sample does not exist', extra=sample_info)
return
#is it already loaded, let's skip for now
if Result.objects.filter(sample=sample).exists():
log.debug('{0} exists in results'.format(vcf_sample))
else:
log.debug('about to load results for {0}'.format(vcf_sample))
#STSError: Cannot start transition while already in one.
successful = False
while not successful:
try:
with transition(sample, 'Sample Published',
event='Loading Results'):
connection = connections[database]
cursor = connection.cursor()
with open(vcf_path) as fin:
stream = ResultStream(fin, sample_id=sample.id,
vcf_sample=vcf_sample)
columns = stream.output_columns
db_table = Result._meta.db_table
pgcopy_batch(stream, db_table, columns, cursor,
database)
# Update result count
sample.count = sample.results.count()
sample.published = True
sample.save()
successful = True
except:
log.error('STS errors')
time.sleep(10)
vcf_info = manifest.section('vcf')
# Absolute path relative to the MANIFEST directory
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
# Compare expected MD5 (in manifest) to the file MD5
if 'md5' in vcf_info:
vcf_md5 = checks.file_md5(vcf_path)
if vcf_md5 != vcf_info['md5']:
log.error('VCF file MD5 does not match expected in manifest',
extra={'manifest_path': manifest_path})
# Existing samples by the same name of a previous version are unpublished
# now that is is ready to be published.
count = Sample.objects.filter(
name__iexact=sample.name, project=sample.project, batch=sample.batch,
version__lt=sample.version).update(published=False)
if count:
log.info('{0} previous versions unpublished for {1}'
.format(count, sample))
def load_samples(manifest_path, database, **kwargs):
manifest = ManifestReader(manifest_path)
# Ensure the sample is marked to be loaded..
if not manifest.marked_for_load():
log.info('Sample not marked for load',
extra={
'manifest_path': manifest_path,
})
return
# Ensure the sample section is valid..
if not check_sample_section(manifest):
log.info('Manifest sample section is not valid',
extra={
'manifest_path': manifest_path,
})
return
# [sample]
# project = PCGC
# batch = OTHER
# sample = 1-03131
# version = 1
sample_info = manifest.section('sample')
vcf_info = manifest.section('vcf')
# ignore whatever sample is listed in the manifest and scan the vcf for samples
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
with open(vcf_path) as file_obj:
log.debug("opening {0} in load_samples".format(vcf_path))
reader = vcf.Reader(file_obj, preserve_order=False)
samples = reader.samples
if 'sample' in sample_info:
pretty_names = sample_info['sample'].split(',')
else:
pretty_names = samples
if len(samples) != len(pretty_names):
log.info(
"Length of comma-delimited samples field in manifest does not match the length of samples in {0}"
.format(vcf_info['file']))
return
# Create the sample (and batch and project if needed)..
num_created = 0
num_skipped = 0
for pretty_name, vcf_sample in zip(pretty_names, samples):
log.debug("trying to create {0} sample record".format(vcf_sample))
sample, created = create_sample(sample_name=pretty_name,
vcf_colname=vcf_sample,
batch_name=sample_info['batch'],
project_name=sample_info['project'],
version=sample_info['version'])
log.debug("{0} created".format(sample))
if created:
num_created += 1
sts.transition(sample, 'Sample Record Created')
else:
num_skipped += 1
# Create a manfiest object for the sample if one does not exist
if created or not SampleManifest.objects.filter(
sample=sample).exists():
sample_manifest = SampleManifest(sample=sample)
sample_manifest.load_content(manifest_path)
sample_manifest.save()
sts.transition(sample, 'Sample Manifest Created')
# Publish to channel that this manifest is eligible for processing
# downstream..
#if num_created>0 or kwargs.get('force', False):
SAMPLE_CHANNEL.publish(manifest_path=manifest_path, database=database)
# Returns whether the sample has been created
load_dict = {'created': num_created, 'skipped': num_skipped}
return load_dict
def load_results(manifest_path, database, **kwargs):
manifest = ManifestReader(manifest_path)
if not manifest.marked_for_load():
log.info('Sample not marked for load',
extra={
'manifest_path': manifest_path,
})
return
# Ensure the sample section is valid..
if not check_sample_section(manifest):
log.info('Manifest sample section is not valid',
extra={
'manifest_path': manifest_path,
})
return
sample_info = manifest.section('sample')
vcf_info = manifest.section('vcf')
# ignore whatever sample is listed in the manifest and scan the vcf for samples
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
with open(vcf_path) as file_obj:
log.debug("opening {0} in load_samples".format(vcf_path))
reader = vcf.Reader(file_obj, preserve_order=False)
samples = reader.samples
if 'sample' in sample_info:
pretty_names = sample_info['sample'].split(',')
else:
pretty_names = samples
for pretty_name, vcf_sample in zip(pretty_names, samples):
try:
sample = Sample.objects.get(
name__iexact=pretty_name,
batch__name__iexact=sample_info['batch'],
project__name__iexact=sample_info['project'],
version=sample_info['version'])
except Sample.DoesNotExist:
log.error('Sample does not exist', extra=sample_info)
return
#is it already loaded, let's skip for now
if Result.objects.filter(sample=sample).exists():
log.debug('{0} exists in results'.format(vcf_sample))
else:
log.debug('about to load results for {0}'.format(vcf_sample))
#STSError: Cannot start transition while already in one.
successful = False
while not successful:
try:
with transition(sample,
'Sample Published',
event='Loading Results'):
connection = connections[database]
cursor = connection.cursor()
with open(vcf_path) as fin:
stream = ResultStream(fin,
sample_id=sample.id,
vcf_sample=vcf_sample)
columns = stream.output_columns
db_table = Result._meta.db_table
pgcopy_batch(stream, db_table, columns, cursor,
database)
# Update result count
sample.count = sample.results.count()
sample.published = True
sample.save()
successful = True
except:
log.error('STS errors')
time.sleep(10)
vcf_info = manifest.section('vcf')
# Absolute path relative to the MANIFEST directory
vcf_path = os.path.join(os.path.dirname(manifest_path), vcf_info['file'])
# Compare expected MD5 (in manifest) to the file MD5
if 'md5' in vcf_info:
vcf_md5 = checks.file_md5(vcf_path)
if vcf_md5 != vcf_info['md5']:
log.error('VCF file MD5 does not match expected in manifest',
extra={
'manifest_path': manifest_path,
})
# Existing samples by the same name of a previous version are unpublished
# now that is is ready to be published.
count = Sample.objects.filter(
name__iexact=sample.name,
project=sample.project,
batch=sample.batch,
version__lt=sample.version).update(published=False)
if count:
log.info('{0} previous versions unpublished for {1}'.format(
count, sample))